Question
Consider the following multiple sequence alignment of four DNA sequences. $\begin{matrix}A & C & T & A \\ A & C & T & G \\ A & G & T & C \\ A & G & C & T \end{matrix} $ Shannon's entropy of the above alignment is ________.
To compute Shannon's entropy for the given DNA sequence alignment, we follow these steps:
- Collect Column Frequencies: Each column in the alignment needs to be analyzed to find the frequency of each nucleotide (A, C, G, T). For instance:
| Position | Nucleotides | Frequencies |
|---|---|---|
| 1 | A, A, A, A | A=4/4 |
| 2 | C, C, G, G | C=2/4, G=2/4 |
| 3 | T, T, T, C | T=3/4, C=1/4 |
| 4 | A, G, C, T | A=1/4, G=1/4, C=1/4, T=1/4 |
- Compute Shannon's Entropy for Each Column: The formula for Shannon's entropy \(H\) for a column is \(-\sum (p_i \cdot \log_2(p_i))\), where \(p_i\) is the frequency of nucleotide \(i\) in that column.
- Column 1: \(- (1 \cdot \log_2(1)) = 0\)
- Column 2: \(- (0.5 \cdot \log_2(0.5) + 0.5 \cdot \log_2(0.5)) = 1\)
- Column 3: \(- (0.75 \cdot \log_2(0.75) + 0.25 \cdot \log_2(0.25)) = 0.81\)
- Column 4: \(- (0.25 \cdot \log_2(0.25) + 0.25 \cdot \log_2(0.25) + 0.25 \cdot \log_2(0.25) + 0.25 \cdot \log_2(0.25)) = 2\)
- Calculate Total Entropy: The total entropy \(H_{total}\) is the sum of the individual entropies: \(H_{total} = 0 + 1 + 0.81 + 2 = 3.81\)
The computed Shannon's entropy is 3.81, which falls within the expected range of 3.8 to 3.82.
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Important Questions from Molecular Structure of Genes and Chromosomes
- All pseudogenes DO NOT code for a __________.
- C-value paradox refers to
- DNA sample collected from an unidentified bacterial species (Y) contains 13% of adenine. The G+C content (in percentage) of Y is ________
The contour length of a B-DNA molecule that encodes a bacterial protein of 33 kDa is _________ nm.
Consider the average molecular weight of an amino acid as 110 Da and helix rise per base pair for B-DNA as 0.34 nm.
(Round off to the nearest integer)
- Which of the following methods is/are used for identifying histone modifications?
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